tbuckley/cabot-search huggingface dataset:
MODL-35. BIOENGINEERED HYDROGEL AND BLOOD BRAIN BARRIER-ON-A-CHIP SYSTEM TO STUDY GLIAL CELL ACTIVATION AND BLOOD BRAIN BARRIER DYSFUNCTION IN GLIOBLASTOMA
Authors: Thomas dePalma, Kennedy Hughes, David Fraas, Marie Tawfik, Colin Hisey, Aleksander Skardal
Journal: Neuro-Oncology (2023)

Abstract Treatments for glioblastoma (GBM) are limited leading to short patient life expectancies after diagnosis. Current preclinical models of GBM fail to accurately replicate the function of the blood brain barrier (BBB) and the extreme heterogeneity of the GBM tumor hindering the drug development process. Therefore, there is a pressing need for improved model systems to study how different GBM subpopulations interact with glial cells and the BBB. To build such a model, we first focused on designing a 3D extracellular matrix-based hydrogel biomaterial that would support human astrocytes and a functional BBB. The hydrogel chosen for these studies is composed of functionalized hyaluronic acid (HA) and gelatin and has similar mechanical properties to the human brain. Using confocal imaging and qPCR, we have shown that astrocytes encapsulated in this hydrogel have greater branching and express fewer markers of activation compared to astrocytes grown in commonly used 3D biomaterials such as collagen I and Matrigel. Treatment with inflammatory cytokines and GBM cell derived extracellular vesicles (EVs) revealed that astrocytes in this environment display the activation and inflammatory phenotypes observed in vivo in GBM. Next, this hydrogel biomaterial was deployed in a bioengineered BBB-on-a-chip. We have shown that this system supports the formation of 3D microvessel structures with human brain endothelial cells, pericytes, and astrocytes that accurately mimic the function of the human BBB. Studies using this BBB-on-a-chip have shown that invasive glioma stem cells alter BBB permeability influencing the transport of certain therapeutics to the tumor site. We are now beginning to test how various subpopulations of GBM tumor cells behave in this model and how changes to glial cells and the BBB impact drug delivery and efficacy. This study shows that engineered in vitro models can provide critical insight into disease mechanisms and inform treatment design in GBM.
NIMG-83. ELUCIDATING INTRA-TUMORAL HETEROGENEITY AND DISTINCT RADIOMIC FEATURES IN GLIOBLASTOMA METHYLATION SUBCLASSES
Authors: Yuji Matsumoto, Jose Garcia, Anahita Fathi Kazerooni, Zied Abdullaev, Omkar Singh, Christos Davatzikos, Kenneth Aldape, MacLean P Nasrallah
Journal: Neuro-Oncology (2023)

Abstract Glioblastoma, IDH-wildtype (GBM), is characterized by the inter- and intra-tumoral molecular heterogeneity. Genome-wide DNA methylation profiling has recently emerged as a promising tool offering complementary value to the classification of central nervous system tumors. In adult GBM patients, the most common methylation subclasses comprise RTK I, RTK II, and MES. We hypothesize that quantification of intricate and spatially complex radiomic features extracted from multi-parametric MRI (mpMRI) is informative to non-invasively determining characteristics of GBM methylation subclasses and their heterogeneity. In this study, mpMRI scans (T1, T1-Gd, T2, T2-FLAIR, DSC, DTI) of newly diagnosed 23 GBM patients were retrospectively collected. We derived 6339 radiomic features, including histograms, morphologic and textural descriptors. For each case, 3-4 multiple samplings from different parts of the tumor were conducted. DNA was extracted from FFPE for each of sample and analyzed for genome-wide DNA methylation patterns using the Illumina EPIC array. Classification of methylation subclasses was performed using the MNP brain tumor classifier v12b6 of the DKFZ. Analysis of variance (ANOVA) with Bonferroni correction was employed to extract subclass-specific radiomic features. Of the 23 patients, 7 indicated intra-tumoral heterogeneity in methylation subclasses. We identified 68 radiomic features (p&amp;lt; 0.05) and 12 radiomic features (p&amp;lt; 0.01) that showed statistically significant differences among the methylation subclasses as determined by ANOVA with Bonferroni correction. A heatmap illustrating the relationships between subclasses and extracted radiomic features displayed distinct trends among subclasses and between heterogeneous and homogeneous cases within the same subclass. Our findings suggest the presence of heterogeneity within methylation subclasses and distinctive imaging patterns for each subclass. These findings potentially pave the way for a more personalized approach to glioblastoma management, highlighting the importance of further validation through the analysis of additional cases.
RADT-33. ANALYSIS OF PATIENTS DIAGNOSED WITH ATYPICAL TERATOID RHABDOID TUMOR OF BRAIN AT TERTIARY CARE CENTER
Authors: Setu Shah, Maitrik Mehta, Akash Pandya, Ankita Parikh
Journal: Neuro-Oncology (2023)

Abstract Atypical Teratoid Rhabdoid Tumor (ATRT) of brain is highly malignant neoplasm with incidence of 1-2% among all pediatric CNS tumors characterized by mutations and subsequent inactivation of SMARCB1 (INI1, hSNF5) gene with dismal prognosis of about 6-18 months. On retrospective analysis of patients between 2010-2021 from Medical Record Department, only five cases of ATRT brain were retrieved. All patients were of pediatric age group (6 yr/F, 2yr/M, 6yr/F, 4yr/F, and 1yr/M – Median 4 yrs). On radiological findings, in four patients lesion was primarily in brain and in one patient with diffuse leptomeningeal enhancement. Three patients underwent craniotomy and gross total excision, and, in 2 patients only biopsy was done. In molecular analysis immunohistochemistry (IHC) markers were as follows. In all patients Vimentin and Synaptophysin were positive. EMA was positive in 3 patients, GPAP was positive in 3 patients, CD99 was positive in 2 patients, AE1 was positive in 2 patients. A specific marker for ATRT (INI1 loss) was seen in 3 patients. In other patients INI1 assessment could not be done. In two patients CSF cytology was negative, and, in all patients bone marrow examination was normal. One patient (4yr/F) received local radiotherapy with concurrent Vincristine based chemotherapy and lost to follow up (after 1 year of treatment). One patient (6yr/F) received vincristine based chemotherapy and local palliative radiotherapy and expired (after 1 month of treatment). One patient (6yr/F) received St Jude HR/IRS III protocol chemotherapy and craniospinal irradiation (CSI) and is still on follow up (total follow up period – 9 years). Two patients did not take any kind of treatment in whom one patient expired, another lost to follow up. Looking at rarity of tumors and with the review of literature, multiagent chemotherapy and Craniospinal irradiation seems to be promising approach for treatment of ATRT brain.
ANGI-04. IKIP SUPPRESSES MIGRATION AND INVASION OF GLIOBLASTOMA BY DOWNREGULATING THBS1/FAK SIGNALING
Authors: Hao Liu, Yanjia Hu, Zhaoying Zhu
Journal: Neuro-Oncology (2023)

Abstract BACKGROUND The role of the inhibitor of NF-κB kinase-interacting protein (IKIP) in glioblastoma (GBM) migration and invasion remains poorly understood, despite its known involvement in the negative regulation of NF-κB signaling and inflammation. This study aimed to investigate the impact of IKIP on GBM metastasis and elucidate the underlying molecular mechanisms. METHODS Expression levels of IKIP were analyzed in gliomas and normal brain tissues using bioinformatic analysis of public databases and immunohistochemical staining of clinical samples. Transwell and wound healing assays were employed to assess the migration and invasion of GBM cell lines. RNA sequencing was conducted to unravel the molecular pathways involved. RESULTS Bioinformatic analysis revealed a significantly higher expression of IKIP in GBM compared to normal brain tissues, and its upregulation was associated with a poor prognosis in glioma patients. However, immunohistochemical and immunofluorescent staining demonstrated the downregulation of IKIP in GBM. Furthermore, functional assays demonstrated that IKIP overexpression suppressed the migratory and invasive capabilities of GBM cell lines, whereas IKIP knockdown enhanced migration and invasion. Mechanistically, IKIP overexpression downregulated THBS1 at the transcriptional level, resulting in the inhibition of THBS1/FAK signaling. CONCLUSIONS This study provides evidence for the first time that IKIP exerts inhibitory effects on GBM migration and invasion by downregulating THBS1/FAK signaling. These findings shed light on the complex mechanisms underlying GBM progression and identify IKIP as a potential therapeutic target for GBM invasion.
PATH-21. GPX4 IS CRUCIALLY IMPLICATED IN THE PATHOBIOLOGY OF GLIOBLASTOMA AND A PUTATIVE ACTIONABLE TARGET
Authors: Suvendu Purkait, Minakshi Behera, Rabi N Sahu, Amit Ghosh
Journal: Neuro-Oncology (2023)

Abstract BACKGROUND Glioblastoma(GBM) is the most common malignant primary brain tumor with a dismal prognosis. Glutathione-mediated inhibition of the ferroptotic form of cell death is crucially implicated in various malignancies, which is principally regulated by glutathione peroxidase 4 (GPX4). However, there is limited data on GBM. The present study evaluated the expression of GPX4 in GBM and its implications in tumor biology, clinical outcome, and therapeutic potentials. METHODS The mRNA and protein expression was assessed by qRT-PCR and immunohistochemistry, respectively, in 75 cases of adult hemispheric GBMs (IDH wild type). For comparison, 21 lower-grade astrocytomas (IDH-mutant, grade-2/3) [LGA] and 20 cases were also evaluated. In-vitro analysis was performed on U87MG and LN229 glioma cell line. RESULTS The mRNA expression of GPX-4 was significantly higher in GBM than LGA, and normal brain (NB) [p-values 0.028, and 0.001, respectively]. Normal brain cases were negative for GPX4. Almost half of the GBMs (49.3%) showed strong immunoreactivity, which was higher than LGAs (23.8%) [p-value -0.04]. Inhibition of GPX-4 in-vitro by 1S-RSL3 &amp; FIN56 was associated with decreased cell survival, proliferation, migration, invasion, and increased cell death. GPX-4 expression was not significantly associated with overall survival in GBM. CONCLUSION GPX-4 is crucial for the tumor cells' survival and aggressive biological behavior. Considering its immune-positivity only in the neoplastic cell and strong positivity in GBM it may be a useful adjunct to the diagnosis. The present study emphasized its role as a potential therapeutic target in the form of 1S-RSL3 &amp; FIN56.
PATH-12. CONTEMPORARY MOLECULAR LANDSCAPE, SURVIVAL, AND PROGNOSTIC FACTORS IN OVER 4,000 GLIOMAS
Authors: Hia Ghosh, Ruchit Patel, Eleanor Woodward, Noah Greenwald, Varun Bhave, Eduardo Maury, Samantha Hoffman, Yvonne Li, Hersh Gupta, Liam Spurr, Mehdi Touat, Frank Dubois, Andrew Cherniack, Gino Cioffi, E Antonio Chiocca, David Reardon, Patrick Wen, David Meredith, Sandro Santagata, Jill Barnholtz-Sloan, Keith Ligon, Rameen Beroukhim, Wenya Linda Bi
Journal: Neuro-Oncology (2023)

Abstract INTRODUCTION Molecular glioma classification and advances in treatment modalities have expanded therapeutic options for patients. We sought to capture the genomic landscape, prognostic features, and contemporary outcomes of gliomas. METHODS We assembled patients from TCGA (n=770) and multi-institutional datasets (n=3,546) with somatic mutations and copy number/structural variants. All gliomas were classified using molecular definitions (WHO 2021/cIMPACT-NOW). We identified correlations between genes through permutations testing and prognostic features through multivariate cox models with backwards elimination. RESULTS We analyzed 4,316 patients (median age 52yrs, 41% female), including 2,155 glioblastoma, 1,199 IDH1/2-mutant astrocytoma, 531 oligodendroglioma, and 343 other IDH1/2-wiltype gliomas. Molecular classification shifted 27.2% of gliomas from their original histopathologic designation. Canonical alterations categorized glioma subtypes, showing unique correlations with clinical features and mutual exclusivity of alterations in tumorigenic pathways. 2,433 patients had clinical outcomes: 1,296 glioblastomas, 584 IDH1/2-mutant astrocytoma, and 327 oligodendrogliomas. Patients from contemporary institutional cohorts had improved overall survival compared to TCGA patients: glioblastoma (non-TCGA:17.9mo,TCGA:15.0mo,p&amp;lt; 0.0001), IDH1/2-mutant astrocytoma (non-TCGA:180mo,TCGA: 87.9mo,p=0.0002), and oligodendroglioma (non-TCGA: not reached,TCGA:135mo,p&amp;lt; 0.0001). In contemporary cohorts, median survival in grade 2-3 IDH1/2-mutant astrocytoma (180.3mo) was double that of grade 4 (75.4mo, p&amp;lt; 0.0001). In GBM and oligodendrogliomas, patients &amp;gt;65yrs had worse outcomes than patients 20-64yrs (p&amp;lt; 0.001). In glioblastoma, age (HR:1.03), CDKN2A/B homozygous deletion (HR:1.22), and NF1 alterations (HR:1.31) were negatively prognostic. Chemotherapy (HR:0.64), MGMT-methylation (HR:0.44), 19q-gain (HR:0.70), and non-TCGA cohort (HR:0.54,HR:0.34) were positively prognostic. In IDH1/2-mutant astrocytoma, CDKN2A/B homozygous deletion (HR:2.75), CCND2 alteration (HR:2.89), EGFR amplification (HR:2.93), PDGFRA alteration (HR:2.87), 9p-loss (HR:3.09), and 10q-loss (HR:1.99) were negatively prognostic; white race was the only prognostically positive feature (HR:0.35). CONCLUSIONS Overall survival in gliomas has improved over time. We corroborated canonical features and identified new prognostic features that are subtype-specific. The unique molecular profiles across glioma subtypes provide insight into biological drivers that influence heterogenous clinical outcomes.
RADT-42. STRATEGIES FOR TREATING RECURRENT GERM CELL TUMORS IN PATIENTS WHO HAVE UNDERGONE PRIOR CHEMORADIOTHERAPY AGAINST PRIMARY GERMINOMA
Authors: Fumiyuki Yamasaki, Yasuyuki Kinoshita, Takeshi Takayasu, Ushio Yonezawa, Akira Taguchi, Shumpei Onishi, Iori Ozono, Novita Ikbar Khairunnisa, Ryosuke Dowaki, Nobutaka Horie
Journal: Neuro-Oncology (2023)

Abstract BACKGROUND Germinoma patients are thought to have a favorable prognosis due to their high sensitivity to chemotherapy and radiotherapy. However, it is also known that germinoma is at risk of recurrence after a long course of disease. Despite excellent sensitivity to chemotherapy and radiotherapy, there is no established standard treatment for patients with recurrent germinoma. METHODS Fourteen patients with recurrent germinoma treated in our institution from 1989 to 2022 were included in this retrospective study. All patients were treated for primary tumor with carboplatin-etoposide and 23.4 Gy of whole ventricle/whole brain irradiation. Twelve patients were treated at our institution at primary and first recurrence, and three patients were referred to our institutional for management against recurrent tumors. Medical records were examined to determine the course of the disease at the time of initial onset, the first recurrence, and the following course, including recurrence and survival. RESULTS There were 12 male and 2 female patients with recurrent germinoma, age at initial onset ranged from 11 to 29 years (median 18.5 years), and age at first recurrence ranged from 16 to 36 years (median 23.5 years). The time from the date of treatment initiation against primary tumor to first confirmed recurrence ranged from 4.2 to 272 months (median 79 months). Eleven patients had recurrences outside the irradiation field, with six experiencing spinal recurrence. Thirteen patients received chemotherapy, and 12 patients had radiotherapy, including eight patients treated with craniospinal irradiation (CSI). There were no reported cases of recurrence or mortality in the CSI-treated group. In contrast, the median PFS and OS in the group that did not receive CSI were 12 and 36 months, respectively, which were significantly different from the CSI-treated group (P &amp;lt; 0.05). CONCLUSION Our findings suggest that CSI has an important role in reducing the likelihood of future recurrence.
EPCO-29. SEXUALLY DIMORPHIC EFFECT OF H-FERRITIN GENETIC MANIPULATION ON SURVIVAL AND IMMUNE CELL INFILTRATION IN A MOUSE MODEL OF GLIOBLASTOMA
Authors: Bhavyata (Pandya) Shesh, Vonn Walter, Becky Slage-Webb, Elizabeth Neely, James R Connor
Journal: Neuro-Oncology (2023)

Abstract Iron plays a crucial role in promoting tumor growth. Recent research has shown that H-ferritin (FTH1), traditionally recognized as an iron storage protein, can transport iron to GBM cancer stem cells, reducing their invasion activity. Moreover, binding of extracellular FTH1 to human GBM tissues, and brain iron delivery in general, has been found to have a sex bias. This raises questions addressed in this study about whether H-ferritin levels extrinsic to the tumor can affect tumor cell pathways and if this impact is sex-specific. Systemic Fth1+/- mice were orthotopically implanted with mouse GBM cells (GL261). Littermate Fth1 +/+ mice were controls. Survival was evaluated and the tumors were subjected to next-generation sequencing protocols. We analyzed resulting data utilizing murine Microenvironment Cell Population (mMCP) method. mMCP estimates abundance of tissue infiltrating immune and stromal populations based on cell-specific gene signatures. Female Fth1+/- mice had significantly poorer survival than control females. Fth1 genetic status had no effect on survival in males. mMCP analysis revealed a significant reduction in T cells and CD8+ T cell infiltration tumors of Fth1+/- females as compared to Fth1+/+. Mast and fibroblast cell infiltration was increased in females and males with Fth1+/- background, respectively, compared to Fth1+/+ mice. Genetic manipulation of Fth1 which leads to reduced systemic levels of FTH1 protein had a sexually dimorphic impact on survival. Fth1+/- significantly worsened survival in females but not in male GBMs. Furthermore, genetic manipulation of Fth1 significantly affected tumor infiltration of T-cells, CD8+ T cells, fibroblasts, and mast cells in a sexually dimorphic manner. These results demonstrate a role for FTH1 and presumably iron status in establishing the tumor cellular landscape that ultimately impacts survival and further reveals a sex bias that may inform the population studies showing a sex effect on the prevalence of brain tumors.
TMIC-77. UNVEILING THE DEPTHS: EXPLORING DIFFUSE MIDLINE GLIOMA, TUMORIGENESIS, AND RADIATION RESISTANCE
Authors: Palak Patel, Bharti Kukreja, Brian Kalish, Sanja Pajovic, Cynthia Hawkins
Journal: Neuro-Oncology (2023)

Abstract Diffuse Midline Glioma (DMG) is a highly aggressive form of brainstem cancer that primarily affects children, leading to a grim prognosis and limited treatment options. Despite extensive research efforts, many crucial aspects of DMG development and progression remain poorly understood. One significant knowledge gap lies in comprehending the invasive nature of DMG cells, which enables their escape from the primary tumor site and dissemination to other regions of the brain. Additionally, understanding the molecular basis that drives this invasive behavior is essential but remains largely unexplored, necessitating further investigation. To address these critical knowledge gaps, we have generated one of the largest single-cell multi-omic datasets ( &amp;gt;300,000 cells) specifically focusing on pons development in humans and its relation to DMG. This dataset provides a valuable resource for investigating the intricacies of tumorigenesis and the development of resistance to radiation therapy. Comprehensive analyses of this dataset shed light on the molecular events driving DMG progression and radiation resistance, ultimately paving the way for the discovery of novel therapeutic targets and the development of innovative strategies to combat this devastating pediatric cancer. In summary, our study aims to deepen our understanding of DMG by elucidating the mechanisms associated with histone mutations, unraveling the invasive behavior of DMG cells, and exploring the factors contributing to radiation resistance. Through these endeavors, we hope to make significant advancements in the field and improve the outcomes for patients affected by DMG.
TMET-01. THERAPEUTIC TARGETING OF CROSSTALK BETWEEN MITOCHONDRIAL FITNESS AND CELL ADHESION/MIGRATION IN DIFFUSE MIDLINE GLIOMA (DMG)
Authors: Rodrigo Cartaxo, Sunjong Ji, Kallen Schwark, Carl Koschmann
Journal: Neuro-Oncology (2023)

Abstract Diffuse midline gliomas (DMGs) are aggressive tumors characterized by infiltration into normal midline brain tissue, hindering surgical resection and contributing to overall morbidity and mortality. To study which genes are driving this invasive phenotype, we established a novel two-step pooled whole genome CRISPR-Migration screen for DMG primary cell cultures (n = 3) derived from patients. After selecting for genes critical for cell survival, each cell line was seeded in the upper chamber of a transwell assay optimized for DMG cells to promote complete serum-free cell attachment and migration through laminin, one of the major components of the blood vessels basement membrane. Following sgRNA library sequencing of low and high-migratory populations, we found a strong positive correlation with genes directly involved in the focal adhesion machinery (ITGB1, CRKL, RAPGEF1, PARVA, PTK2, FERMT2). Stable CRISPR knockout of these genes validated significant reduction in adhesion/migration, without affecting proliferation. Interestingly, we also identified in the screen genes controlling different aspects of mitochondrial function (NDUFAF6, PITRM1, MINOS1, MICU3, LIPT1, MRPL38), especially affecting outer-inner mitochondrial membrane integrity. This finding is in line with the higher sensitivity of multiple DMG cell cultures to Bcl-2 family inhibitors, readily prompting apoptosis in combination with sub-lethal doses of various drugs. Agents that specifically modulate mitochondrial oxidative phosphorylation (OXPHOS) (Rotenone, Oligomycin A, Antimycin A) reduced DMG cell migration without affecting proliferation. Surprisingly, silencing of ITGB1 and CRKL led to a marked decrease in glycolysis and OXPHOS levels, again without any changes in proliferation. Additionally, silencing of ITGB1 (primarily responsible for cell adhesion to laminin) led to the decreased expression (RNA) of multiple mitochondrial NADH dehydrogenases, pointing to an intricate bi-directional mechanism connecting mitochondrial fitness to DMG cell migration. Studies are underway to validate these findings in vivo and to determine an optimal therapeutic disruption of this critical DMG malignant phenotype.